GenomeBaser package

Submodules

GenomeBaser.genomebaser module

Genomebaser is a tool to manage complete genomes from the NCBI

GenomeBaser.genomebaser.check_for_deps()

Check if 3rd party dependencies (non-python) exist

Requires:

• rsysnc
• prokka-genbank_to_fasta_db
• cd-hit
• makeblastdb

GenomeBaser.genomebaser.fetch_genomes(target_genus_species, db_base=None)

Use rsync to manage periodic updates

Examples:

>>> fetch_genomes("Escherichia coli")
>>>
>>> fetch_genomes("Klebsiella pneumoniae", "/home/me/dbs/")

Parameters:target_genus_species – the genus species as a string (space delimited) Returns:the database location

GenomeBaser.genomebaser.genbank_to_fasta(db_loc)

Converts GenBank to fasta while naming using the given in the DEFINITION

Examples:

>>> genbank_to_fasta("/home/mscook/dbs/Klebsiella_pneumoniae"

Parameters:db_loc – the fullpath as a sting to the database location (genus species inclusive) Returns:a list of the output fasta files

GenomeBaser.genomebaser.make_prokka(db_loc, genbank_files, target_genus_species)

Make a prokka database of the complete genomes

Parameters:

• db_loc – the fullpath as a sting to the database location (genus species inclusive)
• genbank_files – a list of GenBank files
• target_genus_species – the genus species as a string (space delimited)

GenomeBaser.genomebaser.partition_genomes(db_loc, fasta_files)

Separate complete genomes from plasmids

..warning:: this partitions on the complete_sequence (plasmid) vs

complete_genome (genome) in filename assumption (in DEFINITION) line

Parameters:

• db_loc – the fullpath as a sting to the database location (genus species inclusive)
• fasta_files – a list of fasta files

Returns:

a list of DEFINITION format named GenBank files

Module contents